Job ID = 2590115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:20 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289135 (1.53%) aligned 0 times 14953812 (79.31%) aligned exactly 1 time 3611867 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3521864 / 18565679 = 0.1897 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 19:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 19:54:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:54:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 19:54:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:54:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 19:54:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:54:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:54:44: 1000000 INFO @ Mon, 12 Aug 2019 19:54:45: 1000000 INFO @ Mon, 12 Aug 2019 19:54:47: 1000000 INFO @ Mon, 12 Aug 2019 19:54:50: 2000000 INFO @ Mon, 12 Aug 2019 19:54:52: 2000000 INFO @ Mon, 12 Aug 2019 19:54:54: 2000000 INFO @ Mon, 12 Aug 2019 19:54:56: 3000000 INFO @ Mon, 12 Aug 2019 19:54:58: 3000000 INFO @ Mon, 12 Aug 2019 19:55:02: 3000000 INFO @ Mon, 12 Aug 2019 19:55:02: 4000000 INFO @ Mon, 12 Aug 2019 19:55:05: 4000000 INFO @ Mon, 12 Aug 2019 19:55:08: 5000000 INFO @ Mon, 12 Aug 2019 19:55:09: 4000000 INFO @ Mon, 12 Aug 2019 19:55:12: 5000000 INFO @ Mon, 12 Aug 2019 19:55:15: 6000000 INFO @ Mon, 12 Aug 2019 19:55:17: 5000000 INFO @ Mon, 12 Aug 2019 19:55:19: 6000000 INFO @ Mon, 12 Aug 2019 19:55:21: 7000000 INFO @ Mon, 12 Aug 2019 19:55:24: 6000000 INFO @ Mon, 12 Aug 2019 19:55:26: 7000000 INFO @ Mon, 12 Aug 2019 19:55:28: 8000000 INFO @ Mon, 12 Aug 2019 19:55:32: 7000000 INFO @ Mon, 12 Aug 2019 19:55:33: 8000000 INFO @ Mon, 12 Aug 2019 19:55:34: 9000000 INFO @ Mon, 12 Aug 2019 19:55:40: 9000000 INFO @ Mon, 12 Aug 2019 19:55:40: 8000000 INFO @ Mon, 12 Aug 2019 19:55:40: 10000000 INFO @ Mon, 12 Aug 2019 19:55:46: 10000000 INFO @ Mon, 12 Aug 2019 19:55:47: 11000000 INFO @ Mon, 12 Aug 2019 19:55:47: 9000000 INFO @ Mon, 12 Aug 2019 19:55:53: 11000000 INFO @ Mon, 12 Aug 2019 19:55:54: 12000000 INFO @ Mon, 12 Aug 2019 19:55:55: 10000000 INFO @ Mon, 12 Aug 2019 19:56:00: 13000000 INFO @ Mon, 12 Aug 2019 19:56:00: 12000000 INFO @ Mon, 12 Aug 2019 19:56:02: 11000000 INFO @ Mon, 12 Aug 2019 19:56:06: 14000000 INFO @ Mon, 12 Aug 2019 19:56:07: 13000000 INFO @ Mon, 12 Aug 2019 19:56:10: 12000000 INFO @ Mon, 12 Aug 2019 19:56:13: 15000000 INFO @ Mon, 12 Aug 2019 19:56:13: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:56:13: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:56:13: #1 total tags in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:56:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:56:13: #1 tags after filtering in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:56:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:56:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:56:14: 14000000 INFO @ Mon, 12 Aug 2019 19:56:15: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 19:56:15: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 19:56:15: start model_add_line... INFO @ Mon, 12 Aug 2019 19:56:15: start X-correlation... INFO @ Mon, 12 Aug 2019 19:56:15: end of X-cor INFO @ Mon, 12 Aug 2019 19:56:15: #2 finished! INFO @ Mon, 12 Aug 2019 19:56:15: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:56:15: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05_model.r WARNING @ Mon, 12 Aug 2019 19:56:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:56:15: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:56:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:56:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:17: 13000000 INFO @ Mon, 12 Aug 2019 19:56:20: 15000000 INFO @ Mon, 12 Aug 2019 19:56:21: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:56:21: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:56:21: #1 total tags in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:56:21: #1 tags after filtering in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:56:21: #1 finished! INFO @ Mon, 12 Aug 2019 19:56:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:56:22: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 19:56:22: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 19:56:22: start model_add_line... INFO @ Mon, 12 Aug 2019 19:56:22: start X-correlation... INFO @ Mon, 12 Aug 2019 19:56:22: end of X-cor INFO @ Mon, 12 Aug 2019 19:56:22: #2 finished! INFO @ Mon, 12 Aug 2019 19:56:22: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:56:22: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10_model.r WARNING @ Mon, 12 Aug 2019 19:56:22: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:56:22: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:56:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:56:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:25: 14000000 INFO @ Mon, 12 Aug 2019 19:56:32: 15000000 INFO @ Mon, 12 Aug 2019 19:56:32: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:56:32: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:56:32: #1 total tags in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:56:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:56:33: #1 tags after filtering in treatment: 15043815 INFO @ Mon, 12 Aug 2019 19:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:56:33: #1 finished! INFO @ Mon, 12 Aug 2019 19:56:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:56:34: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 19:56:34: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 19:56:34: start model_add_line... INFO @ Mon, 12 Aug 2019 19:56:34: start X-correlation... INFO @ Mon, 12 Aug 2019 19:56:34: end of X-cor INFO @ Mon, 12 Aug 2019 19:56:34: #2 finished! INFO @ Mon, 12 Aug 2019 19:56:34: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 19:56:34: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20_model.r WARNING @ Mon, 12 Aug 2019 19:56:34: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:56:34: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:56:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:56:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:56:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:56:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.05_summits.bed INFO @ Mon, 12 Aug 2019 19:57:10: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3594 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:57:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:57:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:57:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.10_summits.bed INFO @ Mon, 12 Aug 2019 19:57:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (913 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494997/SRX494997.20_summits.bed INFO @ Mon, 12 Aug 2019 19:57:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。